Natural Computing Series N C C Series Editors: G. Rozenberg Th. Bäck A.E. Eiben J.N. Kok H.P. Spaink Leiden Center for Natural Computing Advisory Board: S. Amari G. Brassard K.A. De Jong C.C.A.M. Gielen T. Head L. Kari L. Landweber T. Martinetz Z. Michalewicz M.C. Mozer E. Oja Gh. Paun° J. Reif H. Rubin A. Salomaa M. Schoenauer H.-P. Schwefel C. Torras D. Whitley E. Winfree J.M. Zurada Junghuei Chen · Nataša Jonoska Grzegorz Rozenberg (Eds.) Nanotechnology: Science and Computation With 126 Figures and 10 Tables 123 Editors Series Editors Junghuei Chen G. Rozenberg (Managing Editor) Department of Chemistry and Biochemistry [email protected] University of Delaware Newark, DE 19716, USA Th. Bäck, J.N. Kok, H.P. Spaink Leiden Institute of Advanced Nataša Jonoska Computer Science Department of Mathematics Leiden University University of South Florida Niels Bohrweg 1 4202 E. Fowler Av., PHY114 2333 CA Leiden, The Netherlands Tampa, FL 33620-5700, USA A.E. Eiben Grzegorz Rozenberg Vrije Universiteit Amsterdam Leiden University The Netherlands Leiden Institute for Advanced Computer Science Niels Bohrweg 1 2333 CA Leiden, The Netherlands Library of Congress Control Number: 2005936799 ACM Computing Classification (1998): F.1, G.2.3, I.1, I.2, I.6, J.3 ISBN-10 3-540-30295-6 Springer Berlin Heidelberg New York ISBN-13 978-3-540-30295-7 Springer Berlin Heidelberg New York This work is subject to copyright. All rights are reserved, whether the whole or part of the material is concerned, specifically the rights of translation, reprinting, reuse of illustrations, recitation, broadcasting, reproduction on microfilm or in any other way, and storage in data banks. Duplication of this publication or parts thereof is permitted only under the provisions of the German Copyright Law of September 9, 1965, in its current version, and permission for use must always be obtained from Springer. Violations are liable for prosecution under the German Copyright Law. Springer is a part of Springer Science+Business Media springer.com © Springer-Verlag Berlin Heidelberg 2006 Printed in Germany The use of general descriptive names, registered names, trademarks, etc. in this publication does not imply, even in the absence of a specific statement, that such names are exempt from the relevant protective laws and regulations and therefore free for general use. Cover Design: KünkelLopka, Werbeagentur, Heidelberg Typesetting: by the Editors Production: LE-TEX Jelonek, Schmidt & Vöckler GbR, Leipzig Printed on acid-free paper 45/3142/YL – 5 4 3 2 1 0 This book is dedicated to Nadrian C. Seeman on the occasion of his 60th birthday This image was created by DADARA Preface Nanotechnology is slowly and steadily entering more and more aspects of our life. It is becoming a base for developing new materials as well as a base for developing novel methods of computing. As natural computing is concerned with information processing taking place in or inspired by nature, the ideas coming from basic interactions between atoms and molecules naturally become part of these novel ways of computing. While nanotechnology and nanoengineering have flourished in recent years, the roots of DNA nanotechnology go back to the pioneering work of Nadrian (Ned) C. Seeman in the 1980s. Many of the original designs and constructions of nanoscale structures from DNA developed in Ned’s lab provided a com- pletely new way of looking at this molecule of life. Starting with the synthesis of the first immobile Holliday junction, now referred to as J1, through the double and triple cross-over molecules, Ned has shown that DNA is a pow- erful and versatile molecule which is ideal for building complex structures at the nanometer scale. Through the years, Ned has used some of the basic DNA motif struc- tures as ‘tinkertoy’ or ‘lego’ units to build a cube, two-dimensional arrays, and various three-dimensional structures, such as Borromean rings, nanome- chanical devices, nano-walkers (robots), etc. All of them were designed and demonstrated originally in Ned’s lab, but then all these ideas and designs were followed up by many other researchers around the world. Adleman’s seminal paper from 1994 provided a proof of principle that computing at a molecular level, with DNA, is possible. This led to a real explosion of research on molecular computing, and very quickly Ned’s ideas concerning the design and construction of nanoscale structures from DNA had a profound influence on the development of both the theoretical and the experimental foundations of this research area. Ned is a scientist and a chemist in the first place. Although Ned can be considered the founder of the DNA nanoengineering field, he has always considered himself as a chemist who is interested in basic science. Therefore, he is still very interested in the basic physical properties of DNA and enzymes VIII Preface that interact with nucleic acids. Ned has been continuously funded by NIH for almost 30 years and is still providing valuable insights into the DNA and RNA biophysical and topological properties as well as the mechanism of homologous recombination between two chromosomal DNAs. Ned’s enormous influence extends also to service to the scientific com- munity. Here one has to mention that Ned is the founding president of the International Society for Nanoscale Science, Computation and Engineering (ISNSCE). The respect that Ned enjoys is also manifested through various honors and awards that he has received — among others the Feynman Prize in Nanotechnology and the Tulip Award in DNA Computing. Besides science, Ned is very much interested in the world around him, e.g., in art. Amazingly, some of this interest has also influenced his scientific work: by studying the work of Escher he got some specific ideas for constructions of DNA-based nanostructures! Ned is an excellent lecturer and has given talks around the world, thereby instigating significant interest and research in DNA nanotechnology and computing. With this volume, which presents many aspects of research in basic sci- ence, application, theory and computing with DNA molecules, we celebrate a scientist who has been a source of inspiration to many researchers all over the world, and to us a mentor, a scientific collaborator, and a dear friend. December 2005 Junghuei Chen Nataˇsa Jonoska Grzegorz Rozenberg Contents Part I DNA Nanotechnology – Algorithmic Self-assembly Scaffolded DNA Origami: from Generalized Multicrossovers to Polygonal Networks Paul W.K. Rothemund............................................ 3 A Fresh Look at DNA Nanotechnology Zhaoxiang Deng, Yi Chen, Ye Tian, Chengde Mao ................... 23 DNA Nanotechnology: an Evolving Field Hao Yan, Yan Liu ............................................... 35 Self-healing Tile Sets Erik Winfree .................................................... 55 Compact Error-Resilient Computational DNA Tilings John H. Reif, Sudheer Sahu, Peng Yin .............................. 79 Forbidding−Enforcing Conditions in DNA Self-assembly of Graphs Giuditta Franco, Nataˇsa Jonoska ...................................105 Part II Codes for DNA Nanotechnology Finding MFE Structures Formed by Nucleic Acid Strands in a Combinatorial Set Mirela Andronescu, Anne Condon .................................121 Involution Solid Codes Lila Kari, Kalpana Mahalingam ...................................137 X Contents Test Tube Selection of Large Independent Sets of DNA Oligonucleotides Russell Deaton, Junghuei Chen, Jin-Woo Kim, Max H. Garzon, David H. Wood ........................................................147 Part III DNA Nanodevices DNA-Based Motor Work at Bell Laboratories Bernard Yurke ...................................................165 Nanoscale Molecular Transport by Synthetic DNA Machines1 Jong-Shik Shin, Niles A. Pierce ....................................175 Part IV Electronics, Nanowire and DNA A Supramolecular Approach to Metal Array Programming Using Artificial DNA Mitsuhiko Shionoya ..............................................191 Multicomponent Assemblies Including Long DNA and Nanoparticles – An Answer for the Integration Problem? Andreas Wolff, Andrea Csaki, Wolfgang Fritzsche ....................199 Molecular Electronics: from Physics to Computing Yongqiang Xue, Mark A. Ratner ...................................215 Part V Other Bio-molecules in Self-assembly Towards an Increase of the Hierarchy in the Construction of DNA-Based Nanostructures Through the Integration of Inorganic Materials Bruno Samor`ı, Giampaolo Zuccheri, Anita Scipioni, Pasquale De Santis 249 Adding Functionality to DNA Arrays: the Development of Semisynthetic DNA–Protein Conjugates ChristofM.Niemeyer ............................................261 Bacterial Surface Layer Proteins: a Simple but Versatile Biological Self-assembly System in Nature Dietmar Pum, Margit S´ara, Bernhard Schuster, Uwe B. Sleytr .........277 1 Adapted with permission (Table 1, Figs 1–3, and associated text) from J. Am. Chem. Soc. 2004, 126, 10834–10835. Copyright 2004 American Chemical Society. Contents XI Part VI Biomolecular Computational Models Computing with Hairpins and Secondary Structures of DNA Masami Hagiya, Satsuki Yaegashi, Keiichiro Takahashi ...............293 Bottom-up Approach to Complex Molecular Behavior Milan N. Stojanovic ..............................................309 Aqueous Computing: Writing on Molecules Dissolved in Water Tom Head, Susannah Gal .........................................321 Part VII Computations Inspired by Cells Turing Machines with Cells on the Tape Francesco Bernardini,